[gmx-users] AFM pulling options

David L. Bostick dbostick at physics.unc.edu
Thu Aug 1 03:26:16 CEST 2002

Hi Justin,

Does it work in parallel yet?


David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall				dbostick at physics.unc.edu
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick

On Wed, 31 Jul 2002, Justin MacCallum wrote:

> Hi Ernesto and Alicia,
> what version of Gromacs are you using?  I have been working on the AFM
> and umbrella sampling code for a while now.  I think I've finally merged
> all of our changes into the CVS tree now, but the changes are not in a
> currently released version of Gromacs, so you'll have to download and
> install the CVS version using the instructions on the website.  The new
> version of the pull code will (optionally) write out the .pdo file as a
> compressed version (with gzip), so you may need to view it with "zcat
> filename.pdo".  It also now prints a header at the top of the file with
> the name of the pulled and reference groups and spring constants, etc.
>  The rest of the data is now in the format "position_of_pulled_group
>   spring_position".  From this you can easily calculate the force vs
> position.
> I have run some tests with the new version of the pull code, but they
> haven't been exhaustive by any means.  If you find any problems please
> let me know and I'll fix them up as soon as I can.
> Justin
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